MolNFT v1 · #121515 · protein
L-amino acid deaminase from proteus vulgaris
5HXW: “L-amino acid deaminase from proteus vulgaris”. X-ray diffraction, 2 ligands (16A, FAD), 20 pockets (best druggability 0.87). MolNFT v1 #121515 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HXW
- Type
- protein
- Length
- 2,585 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-amino acid deaminase
- EC
- 1.4.3.2
- UniProt
- Q9LCB2
- Ligands
- 16A, FAD
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-amino acid deaminase (EC 1.4.3.2) | protein | 433 | 32% helix, 24% strand | Q9LCB2 |
| B | L-amino acid deaminase (EC 1.4.3.2) | protein | 432 | 32% helix, 23% strand | Q9LCB2 |
| C, D, E, F | L-amino acid deaminase (EC 1.4.3.2) | protein | 430 | 33% helix, 24% strand | Q9LCB2 |
Ligands and binding sites
- 16A · Cetyl-trimethyl-ammonium · ligand · 15 copies · chains A, D, B, C, E, F
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.87 | 0.92 | 102 | FAD, 16A |
| 2 | 581 | 0.87 | 0.92 | 83 | FAD, 16A |
| 3 | 867 | 0.86 | 0.88 | 102 | FAD, 16A |
| 4 | 797 | 0.86 | 0.89 | 98 | FAD, 16A |
| 5 | 657 | 0.86 | 0.90 | 66 | empty |
Interfaces
8 interfaces between chains.
- A–C · 784 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 441 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 402 Ų buried · 1 hydrogen bond · protein-protein
- C–F · 392 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 297 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5HXW · L-amino acid deaminase from Proteus vulgaris · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9LCB2
- Elsewhere: RCSB PDB 5HXW · PDBe 5HXW · UniProt Q9LCB2
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